## [1] TRUE
[]{CaRpools.png)
| Screen | Information |
|---|---|
| Screen ID | PILOT001 |
| Screening Date | 2013-11-11 to 2013-11-23 |
| Organism | Homo sapiens |
| Cell Line | HCT116, HCT116 cells were stably transfected with CAS9-GFP (vector: LOTTA). This was done via lentiviral transduction (MOI not determined). Cells were then selected with puromycin. Cells were FACS sorted 2X for homogenous and high GFP, i.e. CAS9 expression. |
| Drug | KillerTRAIL 50 ng / mL |
| Control | DMSO 0,001% |
| Number of Target | ca. 800 |
| Designs per Gene | varies: 10-20 |
| Library | 12K lib, see annotation file (fasta); sgRNA design was based on very simple design rules (G_N19; before NGG PAM) since parameters that can predict efficacy were not known when the oligo lbrary was designed and ordered. |
| Library Reference File | pilot-screen-library |
| NGS | MiSeq, 100 bp single end, Miseq V2 Kit |
MIACCS
The MIACCS-file can be found at
./data/
MIACCS.xls
Description
Apoptosis related genes/Kinome Library in HCT116 Cas9-GFP cells. TRAIL resistance screen.
All file-based output (e.g. tables) is stored in:
./data.
General stats can be found in
TRAILscreen-STATS.xls.
The following read count statistics were calculated for the single datasets.
| Readcount | Control #1 | Control #2 | TRAIL #1 | TRAIL #2 |
|---|---|---|---|---|
| Mean | 79 | 108 | 109 | 109 |
| Median | 51 | 74 | 41 | 39 |
| SD | 90 | 115 | 244 | 260 |
| Min | 0 | 0 | 0 | 0 |
| Max | 1141 | 1304 | 6819 | 8257 |
| # sgRNA not present | 934 | 817 | 1563 | 1573 |
Information of how many sgRNA per gene were not present in the mapped datasets is stored in:
./data/
TRAILscreen_DROPOUT.xls
In brief, the following number of sgRNAs had a read count of 0 in the dataset:
Control #1: 934 missing sgRNAs
Control #2: 817 missing sgRNAs
TRAIL #1: 1563 missing sgRNAs
TRAIL #2: 1573 missing sgRNAs
In depth dataset read count stats can be found in
./data/
TRAILscreen-STATS.xls
These plots show how the read count of the sgRNAs for each dataset is distributed. Depending on the treatment stringency, e.g. in resistance or dropout screens, the data can show asymmetry. However, the major population should be more or less normally distributed.
The following plot shows the read count for each gene normalized to the number of sgRNAs. Spikes indicate a higher read count per sgRNA for this particular gene.
One would expect no outstanding spikes within the untreated data samples, however spikes within the treated datasets indicate a read count enrichment for this particular gene.
If a non-targeting control has been set in the MIACCS file, this control is highlighted in orange color.
These plots provide an overview of the representation of sgRNAs per gene within your data.
Depending on the number of sgRNAs per gene in the library, one would expect a representation of more than 80 % of sgRNAs per gene in the untreated samples. Moreover, genes with a low percentage of present sgRNAs will also show a reduced readcount.
Non-targeting controls are sgRNAs that do either not target the genome at all (so called random or scramble sgRNAs) or target a gene that does not show a phenotype in the screen.
Therefore, the scatter for these, which are highlighted in blue, will be distributed within the main cloud of scatter points.
Non-targeting control: random
SgRNAs targeting genes that will show a phenotype in the screening setup can be used as positive controls.
These will show either an enrichment (in resistance screens) or a depletion (in dropout screens) in the treatment.
Within the scatter
Positive Control: CASP8
Hit analsysis is performed using three different methods:
For each analysis method, separate plots will be created and analysis files will be written to TRAILscreen_HIT-CALLING.xls. See below for further information.
The following adjusted p-values are used to determine significance levels:
| Method | p-value |
|---|---|
| Wilcox | 0.05 |
| DESeq2 | 0.001 |
| MAGeCK | 0.05 |
Wilcox
Within this approach, the read counts of all sgRNAs in one dataset are first normalized by the function set in the MIACCS file. By default, normalization is done by read count division with the dataset median.
Then, the fold change of each population of sgRNAs for a gene is tested against the population of either the non-targeting controls or randomly picked sgRNAs, as defined by the random picks option within the MIACCS file, using a two-sided Mann-Whitney test with FDR correction.
DESeq2
For the DESeq2 analysis implementation, the read counts of all sgRNAs for a given gene are first summed up to increase the available read count.
Then, DESeq2 analysis is perfomed, which includes the estimation of size-factors, the variance stabilization using a parametric fit and a Wald-Test for differnece in log2 fold changes between the untreated and treated data.
More information about this can be found in Love et al.
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Genome Biology 2014
MAGeCK
MAGeCK analysis uses a rank-based model to test for a change in abundance of sgRNAs after median normalization of the dataset.
Further information can be found at the MAGeCK Homepage.
All analysis data can be found in the TRAILscreen_HIT-CALLING.xls file.
For all genes present in the data, the -log10 corrected p-values are plotted to estimate how well the analysis method performed for this screen. A straight line of points with only small differences in the p-value indicates that the analysis method did not perform well. Genes that resulted in a p-value below the threshold set in the MIACCS file are highlighted in red color.
The following genes showed enrichment in the treatment datasets with a p-value smaller than 0.05:
| untreated | treated | foldchange | p.value | |
|---|---|---|---|---|
| BAX | 3.747567 | 21.346353 | 5.542859 | 0.0178241 |
| CASP8 | 4.037869 | 41.292318 | 7.151636 | 0.0178241 |
| PASK | 2.632026 | 7.833771 | 2.575938 | 0.0178241 |
| FADD | 3.765291 | 35.004169 | 7.126894 | 0.0184341 |
According to the value set, the top 5 % enriched genes were:
| untreated | treated | foldchange | p.value | |
|---|---|---|---|---|
| BAX | 3.747567 | 21.346353 | 5.542859 | 0.0178241 |
| CASP8 | 4.037869 | 41.292318 | 7.151636 | 0.0178241 |
| PASK | 2.632026 | 7.833771 | 2.575938 | 0.0178241 |
| FADD | 3.765291 | 35.004169 | 7.126894 | 0.0184341 |
| FN3K | 2.394351 | 6.545106 | 2.767443 | 0.4030853 |
| SPA17 | 2.616958 | 5.136043 | 1.866767 | 0.4030853 |
| CDK5RAP3 | 2.414025 | 4.678275 | 1.865306 | 0.4202992 |
| TNFRSF11A | 2.664088 | 6.650262 | 1.597737 | 0.7848917 |
| IP6K3 | 2.313419 | 5.295556 | 2.520348 | 0.8019777 |
| ABI1 | 2.999779 | 4.458453 | 1.463144 | 0.9671744 |
| ADCK1 | 3.013987 | 5.668811 | 1.713397 | 0.9671744 |
| AKAP6 | 2.124669 | 3.065627 | 1.367359 | 0.9671744 |
| ALPK2 | 2.424144 | 4.293484 | 1.749312 | 0.9671744 |
| AMHR2 | 2.206300 | 7.288762 | 2.761481 | 0.9671744 |
| AURKA | 2.668363 | 3.391432 | 1.368951 | 0.9671744 |
| AVPR1B | 2.980878 | 4.610329 | 1.469106 | 0.9671744 |
| AXL | 3.189164 | 6.108251 | 1.481180 | 0.9671744 |
| BCL2L1 | 2.403153 | 4.073267 | 1.504323 | 0.9671744 |
| BCL2L11 | 2.486840 | 2.879482 | 1.310120 | 0.9671744 |
| BCL2L14 | 1.798592 | 2.359792 | 1.252899 | 0.9671744 |
| BCL6B | 2.150004 | 3.387478 | 1.557439 | 0.9671744 |
| BID | 1.984433 | 3.494241 | 1.451740 | 0.9671744 |
| BIRC3 | 1.266241 | 1.677194 | 1.297998 | 0.9671744 |
| BLK | 2.414149 | 4.606897 | 1.694439 | 0.9671744 |
| BMP2K | 2.725432 | 7.364192 | 2.114134 | 0.9671744 |
| BMPR1A | 2.851042 | 11.049698 | 3.242482 | 0.9671744 |
| BMPR1B | 2.574995 | 6.898140 | 1.993310 | 0.9671744 |
| BNIP2 | 1.795370 | 3.609330 | 1.824645 | 0.9671744 |
| BNIP3 | 2.280309 | 2.488743 | 1.032476 | 0.9671744 |
| CALM3 | 2.950194 | 8.018547 | 2.108928 | 0.9671744 |
| CAMK1G | 3.038230 | 3.284475 | 1.063666 | 0.9671744 |
| CAMK4 | 3.120206 | 4.176575 | 1.298515 | 0.9671744 |
| CAMKK2 | 3.096820 | 5.179529 | 1.571313 | 0.9671744 |
| CARD14 | 2.505785 | 4.410819 | 1.693491 | 0.9671744 |
| CASK | 2.442766 | 3.036390 | 1.270888 | 0.9671744 |
| CDC42BPA | 1.765662 | 2.496069 | 1.478136 | 0.9671744 |
| CDK1 | 2.480657 | 4.789994 | 1.816161 | 0.9671744 |
| CDK10 | 2.357760 | 2.987199 | 1.135816 | 0.9671744 |
| CDK17 | 2.000075 | 7.985030 | 2.652919 | 0.9671744 |
| CDK8 | 2.849182 | 4.568695 | 1.020590 | 0.9671744 |
| CINP | 1.700964 | 2.942366 | 1.646489 | 0.9671744 |
The following genes showed depletion in the treatment datasets with a p-value smaller than 0.05:
No genes showed significant depletion with a p-value lower than 0.05
According to the value set, the top 5 % depleted genes were:
| untreated | treated | foldchange | p.value | |
|---|---|---|---|---|
| MVD | 2.437008 | 2.045153 | 0.8590363 | 0.4030853 |
| CDC42BPG | 2.457555 | 2.076689 | 0.8770324 | 0.8749233 |
| AK1 | 2.354821 | 2.215271 | 0.9615239 | 0.9671744 |
| ALPK3 | 1.759417 | 1.664550 | 0.9308875 | 0.9671744 |
| AZU1 | 2.965272 | 2.961382 | 0.9237615 | 0.9671744 |
| BBC3 | 2.429212 | 2.246981 | 0.9394726 | 0.9671744 |
| BCL2L12 | 3.872529 | 3.402968 | 0.9480240 | 0.9671744 |
| BCL3 | 2.893494 | 2.714992 | 0.9531555 | 0.9671744 |
| BCL9 | 1.593733 | 1.361372 | 0.8862743 | 0.9671744 |
| CAMK2G | 2.710180 | 2.687168 | 0.9540536 | 0.9671744 |
| CDKN1B | 2.097322 | 1.966672 | 0.9655601 | 0.9671744 |
| CHEK1 | 2.554584 | 2.300618 | 0.9370998 | 0.9671744 |
| CSF1R | 3.466243 | 3.247571 | 0.9083817 | 0.9671744 |
| DFFA | 2.417806 | 2.465291 | 0.9844160 | 0.9671744 |
| DGCR14 | 3.287838 | 3.033271 | 0.9585501 | 0.9671744 |
| DUSP2 | 2.424193 | 2.163852 | 0.9824662 | 0.9671744 |
| DUSP6 | 2.394930 | 2.475443 | 0.9775693 | 0.9671744 |
| FASTK | 2.429278 | 2.201806 | 0.9555991 | 0.9671744 |
| GMFB | 2.359733 | 2.326454 | 0.9807980 | 0.9671744 |
| GSK3A | 1.900868 | 1.941428 | 0.9971515 | 0.9671744 |
| ITPKA | 2.607611 | 2.165611 | 0.9336513 | 0.9671744 |
| MAPK3 | 2.309495 | 2.065603 | 0.9843943 | 0.9671744 |
| MAPK7 | 2.961058 | 2.784324 | 0.9896817 | 0.9671744 |
| MPP3 | 1.740669 | 1.618087 | 0.9367596 | 0.9671744 |
| NEK8 | 2.423821 | 2.357821 | 0.9888161 | 0.9671744 |
| NRG3 | 2.387979 | 2.226621 | 0.9159026 | 0.9671744 |
| NTRK1 | 2.441251 | 2.275309 | 0.9450689 | 0.9671744 |
| PAPSS2 | 2.400848 | 2.199667 | 0.9570816 | 0.9671744 |
| PDK4 | 1.965118 | 1.889239 | 0.9622144 | 0.9671744 |
| PFKFB2 | 1.875278 | 1.848614 | 0.9928155 | 0.9671744 |
| PIK3R3 | 2.401635 | 2.197287 | 0.9221953 | 0.9671744 |
| PKMYT1 | 3.075614 | 3.038899 | 0.9667207 | 0.9671744 |
| PRKACB | 2.211535 | 1.700751 | 0.8653760 | 0.9671744 |
| PRKCE | 2.877672 | 2.620680 | 0.9241182 | 0.9671744 |
| PRKCQ | 1.925311 | 1.762508 | 0.9351715 | 0.9671744 |
| PTK6 | 3.124685 | 3.441370 | 0.9576040 | 0.9671744 |
| RIPK1 | 3.451535 | 3.266084 | 0.9424100 | 0.9671744 |
| RPS6KC1 | 2.023408 | 2.026696 | 0.9733447 | 0.9671744 |
| SCYL3 | 2.114794 | 1.976152 | 0.9914523 | 0.9671744 |
| SGK2 | 3.128786 | 2.851614 | 0.8730285 | 0.9671744 |
| SHC1 | 4.391180 | 3.819887 | 0.9400818 | 0.9671744 |
All analysis data can be found in the TRAILscreen_HIT-CALLING.xls file.
For all genes present in the data, the -log10 corrected p-values are plotted to estimate how well the analysis method performed for this screen. A straight line of points with only small differences in the p-value indicates that the analysis method did not perform well. Genes that resulted in a p-value below the threshold set in the MIACCS file are highlighted in red color.
The following genes showed enrichment in the treatment datasets with a p-value smaller than 0.001:
| log2FoldChange | lfcSE | padj | sgRNA | |
|---|---|---|---|---|
| CASP8 | 2.8539899 | 0.1968984 | 0.0000000 | 2 |
| FADD | 2.7466780 | 0.2008926 | 0.0000000 | 4 |
| BAX | 2.0761255 | 0.1951457 | 0.0000000 | 2 |
| RPS6KA5 | 2.0613922 | 0.1993450 | 0.0000000 | 5 |
| CDK17 | 1.9749507 | 0.2098786 | 0.0000000 | 6 |
| HRK | 1.7832227 | 0.1986851 | 0.0000000 | 0 |
| TP53 | 1.7263896 | 0.1990543 | 0.0000000 | 3 |
| BMPR1A | 1.6606699 | 0.1934715 | 0.0000000 | 2 |
| AMHR2 | 1.5964273 | 0.2040561 | 0.0000000 | 3 |
| PRKAR1A | 1.3066797 | 0.1966018 | 0.0000000 | 2 |
| PASK | 1.3056495 | 0.2018553 | 0.0000001 | 2 |
| PRKCH | 1.2768183 | 0.2034549 | 0.0000003 | 4 |
| PRKD3 | 1.2469315 | 0.2049320 | 0.0000009 | 4 |
| PTPRR | 1.1714789 | 0.1988912 | 0.0000031 | 2 |
| FN3K | 1.2257973 | 0.2101826 | 0.0000044 | 2 |
| BMP2K | 1.1356520 | 0.1969679 | 0.0000065 | 2 |
| MDM2 | 1.1155550 | 0.2005697 | 0.0000212 | 3 |
| PRKCZ | 1.1267946 | 0.2027299 | 0.0000217 | 2 |
| PAG1 | 1.2017977 | 0.2167288 | 0.0000233 | 3 |
| BMPR1B | 1.1476671 | 0.2081757 | 0.0000279 | 0 |
| PRKY | 1.1629272 | 0.2119197 | 0.0000322 | 1 |
| MYC | 1.0493447 | 0.1952001 | 0.0000603 | 4 |
| DUSP4 | 1.0685262 | 0.2020427 | 0.0000972 | 5 |
| CSNK2A2 | 1.3577535 | 0.2578919 | 0.0001106 | 2 |
| LMTK3 | 1.0154113 | 0.1953558 | 0.0001587 | 3 |
| MAP2K7 | 1.1032489 | 0.2128120 | 0.0001706 | 1 |
| LATS1 | 1.2426869 | 0.2460336 | 0.0003452 | 1 |
| CALM3 | 1.0844637 | 0.2148274 | 0.0003499 | 2 |
| IP6K3 | 0.9775242 | 0.1947187 | 0.0004042 | 2 |
| RIPK2 | 0.9771641 | 0.1981684 | 0.0006398 | 2 |
According to the value set, the top 5 % enriched genes were:
| log2FoldChange | lfcSE | padj | sgRNA | |
|---|---|---|---|---|
| CASP8 | 2.8539899 | 0.1968984 | 0.0000000 | 2 |
| FADD | 2.7466780 | 0.2008926 | 0.0000000 | 4 |
| BAX | 2.0761255 | 0.1951457 | 0.0000000 | 2 |
| RPS6KA5 | 2.0613922 | 0.1993450 | 0.0000000 | 5 |
| CDK17 | 1.9749507 | 0.2098786 | 0.0000000 | 6 |
| HRK | 1.7832227 | 0.1986851 | 0.0000000 | 0 |
| TP53 | 1.7263896 | 0.1990543 | 0.0000000 | 3 |
| BMPR1A | 1.6606699 | 0.1934715 | 0.0000000 | 2 |
| AMHR2 | 1.5964273 | 0.2040561 | 0.0000000 | 3 |
| PRKAR1A | 1.3066797 | 0.1966018 | 0.0000000 | 2 |
| PASK | 1.3056495 | 0.2018553 | 0.0000001 | 2 |
| PRKCH | 1.2768183 | 0.2034549 | 0.0000003 | 4 |
| PRKD3 | 1.2469315 | 0.2049320 | 0.0000009 | 4 |
| PTPRR | 1.1714789 | 0.1988912 | 0.0000031 | 2 |
| FN3K | 1.2257973 | 0.2101826 | 0.0000044 | 2 |
| BMP2K | 1.1356520 | 0.1969679 | 0.0000065 | 2 |
| MDM2 | 1.1155550 | 0.2005697 | 0.0000212 | 3 |
| PRKCZ | 1.1267946 | 0.2027299 | 0.0000217 | 2 |
| PAG1 | 1.2017977 | 0.2167288 | 0.0000233 | 3 |
| BMPR1B | 1.1476671 | 0.2081757 | 0.0000279 | 0 |
| PRKY | 1.1629272 | 0.2119197 | 0.0000322 | 1 |
| MYC | 1.0493447 | 0.1952001 | 0.0000603 | 4 |
| DUSP4 | 1.0685262 | 0.2020427 | 0.0000972 | 5 |
| CSNK2A2 | 1.3577535 | 0.2578919 | 0.0001106 | 2 |
| LMTK3 | 1.0154113 | 0.1953558 | 0.0001587 | 3 |
| MAP2K7 | 1.1032489 | 0.2128120 | 0.0001706 | 1 |
| LATS1 | 1.2426869 | 0.2460336 | 0.0003452 | 1 |
| CALM3 | 1.0844637 | 0.2148274 | 0.0003499 | 2 |
| IP6K3 | 0.9775242 | 0.1947187 | 0.0004042 | 2 |
| RIPK2 | 0.9771641 | 0.1981684 | 0.0006398 | 2 |
| PRPS1 | 1.0154924 | 0.2099970 | 0.0010360 | 2 |
| MAPK8IP2 | 0.9554903 | 0.2044514 | 0.0023104 | 2 |
| CSNK2A1 | 0.9415114 | 0.2038046 | 0.0029940 | 5 |
| PRKAG3 | 0.9230088 | 0.2009259 | 0.0033866 | 5 |
| NEK11 | 0.9335366 | 0.2033509 | 0.0034314 | 3 |
| TGFBR1 | 0.9607698 | 0.2096900 | 0.0035763 | 2 |
| TNFRSF11B | 0.9509991 | 0.2077597 | 0.0036486 | 0 |
| MAPK13 | 0.9602742 | 0.2100303 | 0.0037378 | 3 |
| MBIP | 0.9025821 | 0.2012146 | 0.0056186 | 5 |
| SEPHS1 | 0.8714230 | 0.1947709 | 0.0059241 | 1 |
| TNFRSF11A | 1.0021224 | 0.2284252 | 0.0088570 | 1 |
The following genes showed depletion in the treatment datasets with a p-value smaller than 0.001:
| log2FoldChange | lfcSE | padj | sgRNA | |
|---|---|---|---|---|
| SMG1 | -1.429982 | 0.2123290 | 0.0e+00 | 7 |
| PRKACB | -1.326844 | 0.2187738 | 1.1e-06 | 4 |
According to the value set, the top 5 % depleted genes were:
| log2FoldChange | lfcSE | padj | sgRNA | |
|---|---|---|---|---|
| SMG1 | -1.4299818 | 0.2123290 | 0.0000000 | 7 |
| PRKACB | -1.3268439 | 0.2187738 | 0.0000011 | 4 |
| DUSP2 | -0.8839585 | 0.2036127 | 0.0109028 | 2 |
| MAPK3 | -0.8874385 | 0.2055074 | 0.0120925 | 4 |
| MVD | -1.0079883 | 0.2337749 | 0.0124369 | 2 |
| HK3 | -0.8896877 | 0.2091965 | 0.0161867 | 2 |
| BCL2L12 | -0.8493349 | 0.2009970 | 0.0182295 | 0 |
| ROCK1 | -0.8921263 | 0.2144381 | 0.0241872 | 3 |
| WIF1 | -0.8396864 | 0.2018872 | 0.0242731 | 3 |
| BBC3 | -0.7995261 | 0.2002468 | 0.0491891 | 2 |
| SGK2 | -0.7987094 | 0.2001047 | 0.0493829 | 2 |
| PRKCQ | -0.8650269 | 0.2190015 | 0.0587241 | 4 |
| CDC42BPG | -0.9735155 | 0.2476437 | 0.0633304 | 1 |
| NRG3 | -0.7790845 | 0.1998423 | 0.0723033 | 3 |
| MPP3 | -0.8573709 | 0.2218129 | 0.0825529 | 4 |
| CDKN1B | -0.7810259 | 0.2039736 | 0.0954487 | 2 |
| MAPK7 | -0.7443061 | 0.1956164 | 0.1051081 | 1 |
| AK1 | -0.7584758 | 0.1999155 | 0.1097052 | 2 |
| CSF1R | -0.7419327 | 0.1957882 | 0.1115685 | 1 |
| ITPKA | -0.9804692 | 0.2588762 | 0.1123445 | 1 |
| CHEK1 | -0.8384986 | 0.2227553 | 0.1231337 | 5 |
| FASTK | -0.8297426 | 0.2226460 | 0.1427661 | 1 |
| SHC1 | -0.8360697 | 0.2249526 | 0.1483839 | 0 |
| ALPK3 | -0.7916102 | 0.2130996 | 0.1493037 | 2 |
| SCYL3 | -0.7831114 | 0.2119499 | 0.1613076 | 3 |
| C9orf96 | -0.7498465 | 0.2060267 | 0.1990927 | 0 |
| PIK3R3 | -0.8057038 | 0.2266208 | 0.2741052 | 3 |
| DGKG | -0.7204221 | 0.2027228 | 0.2753605 | 5 |
| PRKCE | -0.7937112 | 0.2241867 | 0.2892502 | 2 |
| PRKG2 | -0.8289301 | 0.2356366 | 0.3145684 | 7 |
| MASTL | -0.7723763 | 0.2220390 | 0.3629619 | 4 |
| BCL3 | -0.7351915 | 0.2172953 | 0.5119468 | 1 |
| LCK | -0.6660242 | 0.1988919 | 0.5781373 | 1 |
| NTRK1 | -0.7545015 | 0.2277952 | 0.6563060 | 0 |
| NEK8 | -0.6734080 | 0.2042739 | 0.6928860 | 3 |
| TLR1 | -0.7084222 | 0.2149545 | 0.6941480 | 2 |
| PDK4 | -0.7204333 | 0.2189604 | 0.7067081 | 5 |
| TNFRSF4 | -0.8135550 | 0.2473382 | 0.7082275 | 1 |
| PIK3CB | -0.7376748 | 0.2258552 | 0.7653496 | 3 |
| DGCR14 | -0.7534509 | 0.2320389 | 0.8173098 | 5 |
| PKMYT1 | -0.6395897 | 0.1974689 | 0.8398297 | 0 |
All analysis data for MAGeCK can be found in the TRAILscreen_HIT-CALLING.xls file.
For all genes present in the data, the -log10 corrected p-values are plotted to estimate how well the analysis method performed for this screen. A straight line of points with only small differences in the p-value indicates that the analysis method did not perform well. Genes that resulted in a p-value below the threshold set in the MIACCS file are highlighted in red color.
The following genes showed enrichment in the treatment datasets with a p-value smaller than 0.05:
| pos | rank.pos | neg | rank.neg | sgrna.neg.good | sgrna.pos.good | |
|---|---|---|---|---|---|---|
| CASP8 | 0.001650 | 1 | 0.994410 | 804 | 0 | 10 |
| BAX | 0.001650 | 2 | 0.994232 | 775 | 1 | 9 |
| FADD | 0.001650 | 3 | 0.994410 | 792 | 1 | 9 |
| PASK | 0.003713 | 4 | 0.994410 | 800 | 1 | 11 |
According to the value set, the top 5 % enriched genes were:
| pos | rank.pos | neg | rank.neg | sgrna.neg.good | sgrna.pos.good | |
|---|---|---|---|---|---|---|
| CASP8 | 0.001650 | 1 | 0.994410 | 804 | 0 | 10 |
| BAX | 0.001650 | 2 | 0.994232 | 775 | 1 | 9 |
| FADD | 0.001650 | 3 | 0.994410 | 792 | 1 | 9 |
| PASK | 0.003713 | 4 | 0.994410 | 800 | 1 | 11 |
| TYRO3 | 0.659241 | 5 | 0.981079 | 109 | 4 | 9 |
| AMHR2 | 0.659241 | 6 | 0.994410 | 796 | 1 | 5 |
| FN3K | 0.661245 | 7 | 0.994232 | 730 | 2 | 11 |
| PRKY | 0.785149 | 8 | 0.994232 | 479 | 4 | 8 |
| CDK5RAP3 | 0.785149 | 9 | 0.994450 | 807 | 1 | 9 |
| ROR2 | 0.785149 | 10 | 0.994232 | 734 | 3 | 7 |
| BMPR1A | 0.785149 | 11 | 0.994232 | 637 | 3 | 6 |
| DGKI | 0.785149 | 12 | 0.994232 | 609 | 4 | 5 |
| IP6K3 | 0.785149 | 13 | 0.994232 | 678 | 2 | 10 |
| SGK1 | 0.785149 | 14 | 0.994232 | 562 | 2 | 6 |
| CSNK1A1 | 0.785149 | 15 | 0.993066 | 290 | 6 | 2 |
| RPS6KA5 | 0.792340 | 16 | 0.994410 | 802 | 1 | 5 |
| FGFR2 | 0.792340 | 17 | 0.994232 | 435 | 4 | 6 |
| FER | 0.792340 | 18 | 0.994232 | 707 | 2 | 8 |
| GAK | 0.792340 | 19 | 0.994232 | 527 | 2 | 7 |
| MYC | 0.819189 | 20 | 0.994232 | 740 | 2 | 8 |
| NME7 | 0.819189 | 21 | 0.994232 | 359 | 3 | 9 |
| MAP3K13 | 0.903465 | 22 | 0.993066 | 214 | 6 | 8 |
| CDK17 | 0.903465 | 23 | 0.994232 | 533 | 1 | 6 |
| UCK1 | 0.903465 | 24 | 0.994410 | 790 | 2 | 8 |
| SPA17 | 0.903465 | 25 | 0.994232 | 781 | 2 | 9 |
| STK32A | 0.903465 | 26 | 0.994232 | 596 | 1 | 8 |
| MVK | 0.912769 | 27 | 0.994232 | 695 | 2 | 6 |
| BIRC5 | 0.912769 | 28 | 0.993066 | 177 | 5 | 4 |
| MAP2K7 | 0.912769 | 29 | 0.950888 | 62 | 7 | 7 |
| TNFRSF8 | 0.919967 | 30 | 0.993066 | 225 | 4 | 6 |
| RIPK2 | 0.987129 | 31 | 0.994232 | 524 | 3 | 7 |
| MAP2K3 | 0.987129 | 32 | 0.993066 | 137 | 5 | 7 |
| CDK9 | 0.987129 | 33 | 0.994232 | 493 | 3 | 5 |
| DUSP10 | 0.987129 | 34 | 0.994232 | 633 | 1 | 8 |
| LMTK3 | 0.987129 | 35 | 0.994232 | 673 | 2 | 4 |
| TK2 | 0.987129 | 36 | 0.994232 | 602 | 3 | 9 |
| NLK | 0.987129 | 37 | 0.994232 | 663 | 2 | 8 |
| PRKD2 | 0.987129 | 38 | 0.994232 | 444 | 5 | 7 |
| PRPS1 | 0.987129 | 39 | 0.993066 | 247 | 4 | 6 |
| SGK223 | 0.987129 | 40 | 0.993066 | 289 | 6 | 5 |
| SRPK2 | 0.987129 | 41 | 0.994232 | 658 | 2 | 5 |
The following genes showed depletion in the treatment datasets with a p-value smaller than 0.05:
No genes showed significant depletion with a p-value lower than 0.05
According to the value set, the top 5 % depleted genes were:
| pos | rank.pos | neg | rank.neg | sgrna.neg.good | sgrna.pos.good | |
|---|---|---|---|---|---|---|
| TNFRSF13C | 0.996031 | 555 | 0.701894 | 1 | 4 | 1 |
| DYRK2 | 0.987129 | 373 | 0.701894 | 2 | 9 | 4 |
| CDC42BPG | 0.996304 | 803 | 0.701894 | 3 | 9 | 2 |
| CHEK1 | 0.996304 | 777 | 0.701894 | 4 | 6 | 2 |
| RAPGEF3 | 0.987129 | 78 | 0.701894 | 5 | 5 | 6 |
| TNFRSF11A | 0.987129 | 96 | 0.701894 | 6 | 9 | 1 |
| CSF1R | 0.996304 | 784 | 0.701894 | 7 | 8 | 1 |
| PTK6 | 0.996304 | 743 | 0.701894 | 8 | 9 | 3 |
| BMF | 0.996304 | 585 | 0.701894 | 9 | 2 | 4 |
| TESK2 | 0.987129 | 478 | 0.701894 | 10 | 6 | 4 |
| NUAK2 | 0.987129 | 213 | 0.701894 | 11 | 3 | 5 |
| AURKA | 0.987129 | 219 | 0.701894 | 12 | 7 | 3 |
| PRKACB | 0.996304 | 769 | 0.701894 | 13 | 7 | 1 |
| NRG3 | 0.996304 | 724 | 0.701894 | 14 | 8 | 3 |
| TNFRSF13B | 0.987129 | 344 | 0.701894 | 15 | 4 | 2 |
| AZU1 | 0.996304 | 718 | 0.701894 | 16 | 6 | 3 |
| WIF1 | 0.996304 | 799 | 0.701894 | 17 | 7 | 2 |
| MAPK7 | 0.996304 | 678 | 0.701894 | 18 | 8 | 2 |
| HK3 | 0.996304 | 650 | 0.701894 | 19 | 6 | 4 |
| BCL2L12 | 0.996304 | 707 | 0.701894 | 20 | 6 | 2 |
| TP53BP1 | 0.987129 | 395 | 0.701894 | 21 | 2 | 4 |
| ITPKA | 0.996304 | 795 | 0.701894 | 22 | 8 | 2 |
| JAK3 | 0.987129 | 516 | 0.701894 | 23 | 8 | 3 |
| CSNK1A1L | 0.987129 | 451 | 0.736436 | 24 | 7 | 3 |
| PAK7 | 0.987129 | 452 | 0.736436 | 25 | 7 | 5 |
| MAP3K6 | 0.987129 | 350 | 0.790240 | 26 | 5 | 3 |
| CAMK1G | 0.996304 | 600 | 0.790240 | 27 | 6 | 3 |
| PFKFB1 | 0.987129 | 340 | 0.790240 | 28 | 10 | 5 |
| SGK2 | 0.996304 | 786 | 0.790240 | 29 | 6 | 1 |
| PRKAA1 | 0.996304 | 697 | 0.790240 | 30 | 7 | 3 |
| PKMYT1 | 0.996304 | 708 | 0.790240 | 31 | 9 | 3 |
| TSSK3 | 0.996304 | 570 | 0.790240 | 32 | 6 | 3 |
| NTRK3 | 0.987129 | 377 | 0.790240 | 33 | 7 | 3 |
| FASTK | 0.996304 | 703 | 0.790240 | 34 | 8 | 4 |
| AK1 | 0.996304 | 757 | 0.790240 | 35 | 9 | 2 |
| CLK3 | 0.996304 | 635 | 0.808760 | 36 | 9 | 3 |
| MAPKAPK5 | 0.987129 | 514 | 0.808760 | 37 | 7 | 4 |
| PTPRG | 0.996304 | 624 | 0.808760 | 38 | 5 | 4 |
| CDC42SE2 | 0.987129 | 517 | 0.808760 | 39 | 8 | 3 |
| ACVRL1 | 0.996304 | 651 | 0.808760 | 40 | 6 | 4 |
| PAPSS1 | 0.987129 | 527 | 0.808760 | 41 | 8 | 5 |
Genes which showed enrichment or depletion within the individual analysis methods are presented in the following section.
All genes that showed significant enrichment within Wilcox, DESeq2 and MAGeCK with the given p-value cutoffs are highlighted in red color.
All genes that showed significant depletion within Wilcox, DESeq2 and MAGeCK with the given p-value cutoffs are highlighted in blue color.
Moreover, all genes that showed up as significantly enriched or depleted in any of the analysis methods are highlighted in orange color. Genes that showed no significant effect are presented in grey or black color.
The following genes showed enrichment in all three analysis methods.
Within the top enriched hits, the overlap of enriched hits per analysis method is displayed as follows:
ATTENTION
No overlapping depleted genes were found between all three methods.
Therefore, the overlap from the 5 % of genes within all methods is used for plotting possible hit candidates.
We strongly advise you to have a closer look at the individual outputs of the analysis methods and to carefully look at the following candidate genes.
Within the top depleted hits, the overlap of depleted hits per analysis method is displayed as follows:
Scatterplots representing the gene read count as well as sgRNA read count for all overlapping hits are plotted in this section.
If there were signficantly enriched or depleted genes that overlapped in all analysis methods, they will be presented here.
Therefore, the top overlapping hits of each Hit Analysis with a p-value below the thresholds
for each analysis method are highlighted in orange within the scatter plots for all four samples.
In the case that no significantly enriched or depleted genes did overlap in all methods, those that overlapped within the 5 % of top enriched and the top 5 % depleted genes are used.
Therefore, the top overlapping hits of each Hit Analysis are highlighted in orange within the scatter plots for all four samples.
This allows a fast and easy view for single genes and its individual sgRNAs.
Moreover, individual sgRNA effects are plotted as well as the corresponding target sequence.
In this section, the following plots are generated for each hit candidate:
The scatter plots show the median normalized, log read count of each genes/sgRNA. Moreover, the blue lines indicate a read count foldchange of 2, the green lines indicate a read count foldchange of 4.
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) LRG_34
HGNC SYMBOL (links to GeneCards) CASP8
GENE DESCRIPTION
caspase 8, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:HGNC:1509]
GO TERM
MIM GENE DESCRIPTION
CASPASE 8, APOPTOSIS-RELATED CYSTEINE PROTEASE; CASP8;;MORT1-ASSOCIATED CED3 HOMOLOG; MACH;;FADD-HOMOLOGOUS ICE/CED3-LIKE PROTEASE;;FADD-LIKE ICE; FLICE;;MCH5
ENSEMBL PROTEIN ID
LRG_34p2
PROTEIN FAMILY DESCRIPTION
CASPASE PRECURSOR CASP APOPTOTIC PROTEASE MCH ICE APOPTOTIC PROTEASE [CONTAINS CASPASE SUBUNIT CASPASE SUBUNIT
Wilcox p-value: 0.01782408
DESeq2 p-value: 1.063499e-44
MAGeCK p-value: 0.00165
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 2 | CASP8_192_46512 | CASP8 | gatgatgcccttgtctccat | 4.0442283 |
| 3 | CASP8_193_46512 | CASP8 | gagatgtcagctcatagatg | 4.0404115 |
| 9 | CASP8_95_46512 | CASP8 | ggagacaagggcatcatcta | 3.7513973 |
| 7 | CASP8_199_46512 | CASP8 | gacatcgctctctcaggctc | 3.5778575 |
| 10 | CASP8_96_46512 | CASP8 | ggcatcatctatggcactga | 3.4739444 |
| 6 | CASP8_198_46512 | CASP8 | gcaaagtgactggatgtacc | 2.1055251 |
| 1 | CASP8_104_46512 | CASP8 | gcctgagagagcgatgtcct | 1.7201422 |
| 5 | CASP8_197_46512 | CASP8 | ggaaacacagttattcacag | 1.6918053 |
| 11 | CASP8_97_46512 | CASP8 | gagctgacatctcagttcac | 0.8950126 |
| 4 | CASP8_196_46512 | CASP8 | gcagaaagtcagcctcatcc | 0.8529520 |
| 8 | CASP8_218_46512 | CASP8 | gaaggcataaagcaagtttg | 0.0000000 |
| 12 | CASP8_99_46512 | CASP8 | ggagcaaccctatttagaaa | -0.2440090 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000087088
HGNC SYMBOL (links to GeneCards) BAX
GENE DESCRIPTION
BCL2-associated X protein [Source:HGNC Symbol;Acc:HGNC:959]
GO TERM
mitochondrial outer membrane
MIM GENE DESCRIPTION
BCL2-ASSOCIATED X PROTEIN; BAX
ENSEMBL PROTEIN ID
ENSP00000375744
PROTEIN FAMILY DESCRIPTION
APOPTOSIS REGULATOR BAX
Wilcox p-value: 0.01782408
DESeq2 p-value: 1.593957e-23
MAGeCK p-value: 0.00165
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 4 | BAX_36_5982 | BAX | gtccaatgtccagcccatga | 3.6370541 |
| 7 | BAX_45_5982 | BAX | gcgtcccaaagtaggagagg | 3.4780185 |
| 5 | BAX_3_5982 | BAX | gaactgatcagaaccatcat | 3.1659229 |
| 11 | BAX_9_5982 | BAX | gcagaccgtgaccatctttg | 2.6287417 |
| 8 | BAX_46_5982 | BAX | gatggtcacggtctgccacg | 2.4434385 |
| 1 | BAX_10_5982 | BAX | gaccgtgaccatctttgtgg | 2.4213382 |
| 6 | BAX_44_5982 | BAX | gaggaggccgtcctggagac | 1.9233456 |
| 3 | BAX_18_5982 | BAX | gggggtaataaacctccttc | 1.5871055 |
| 9 | BAX_47_5982 | BAX | gagcactcccgccacaaaga | 1.5148023 |
| 2 | BAX_11_5982 | BAX | gctgaggcccccagctgcct | -0.0430781 |
| 10 | BAX_8_5982 | BAX | gacggcctcctctcctactt | -0.3111825 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) LRG_228
HGNC SYMBOL (links to GeneCards) FADD
GENE DESCRIPTION
Fas (TNFRSF6)-associated via death domain [Source:HGNC Symbol;Acc:HGNC:3573]
GO TERM
MIM GENE DESCRIPTION
FAS-ASSOCIATED VIA DEATH DOMAIN; FADD;;FAS-ASSOCIATING PROTEIN WITH DEATH DOMAIN;;MORT1
ENSEMBL PROTEIN ID
LRG_228p1
PROTEIN FAMILY DESCRIPTION
FAS ASSOCIATED DEATH DOMAIN FAS ASSOCIATING DEATH DOMAIN CONTAINING MEDIATOR OF RECEPTOR INDUCED TOXICITY FADD
Wilcox p-value: 0.01843405
DESeq2 p-value: 1.205659e-39
MAGeCK p-value: 0.00165
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 6 | FADD_19_0 | FADD | gcagcatggagaagaggtct | 4.3250217 |
| 1 | FADD_10_3015 | FADD | gcaacctgacagagcgtgtg | 4.0186830 |
| 5 | FADD_18_0 | FADD | gaggcataggaacttgagct | 3.6167997 |
| 7 | FADD_20_0 | FADD | gctccagcagcatggagaag | 3.2846277 |
| 8 | FADD_21_0 | FADD | gtcgttctgctccagcagca | 3.2504992 |
| 11 | FADD_6_0 | FADD | gccgcttgcagaccccgcca | 2.2663642 |
| 9 | FADD_23_3015 | FADD | gcacacgctctgtcaggttg | 2.0061298 |
| 12 | FADD_9_0 | FADD | gctgctggagcagaacgacc | 1.9549099 |
| 2 | FADD_14_0 | FADD | gaaacggctgcggcttcgct | 1.0323283 |
| 3 | FADD_15_0 | FADD | gccgcttgcccagcggccca | 0.3338738 |
| 10 | FADD_4_0 | FADD | ggtggaatccttgggccgct | -0.0800059 |
| 4 | FADD_16_3015 | FADD | gtcctcgatgctgtcgatct | -0.3712259 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000115687
HGNC SYMBOL (links to GeneCards) PASK
GENE DESCRIPTION
PAS domain containing serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:17270]
GO TERM
MIM GENE DESCRIPTION
PAS DOMAIN-CONTAINING SERINE/THREONINE KINASE; PASK;;PAS KINASE;;PASKIN;;KIAA0135
ENSEMBL PROTEIN ID
ENSP00000486149
PROTEIN FAMILY DESCRIPTION
UNKNOWN
Wilcox p-value: 0.01782408
DESeq2 p-value: 7.9517e-08
MAGeCK p-value: 0.003713
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 14 | PASK_110_25236 | PASK | gaatgagcagattcgtttta | 2.5192130 |
| 12 | PASK_10_6309 | PASK | ggccacgttagccggcaagg | 2.3438587 |
| 2 | PASK_0_18927 | PASK | gagcaccacacttcttccta | 2.3183905 |
| 10 | PASK_10_25236 | PASK | gcaagcacgacattaatcct | 1.4918070 |
| 15 | PASK_110_31545 | PASK | gccagcacatcccaaaggta | 1.4773762 |
| 5 | PASK_102_37854 | PASK | gatcagatcttttatgccct | 1.4529940 |
| 4 | PASK_100_31545 | PASK | gttgctaacgacaaagcttg | 1.3469513 |
| 9 | PASK_10_18927 | PASK | gccttggccaaggtcaacac | 1.1772435 |
| 8 | PASK_109_6309 | PASK | gaaataggcatggtgtgcgt | 1.0279086 |
| 11 | PASK_10_31545 | PASK | gcgtgagcttctggccaatc | 1.0060151 |
| 13 | PASK_110_0 | PASK | gctgacctgtcacctgtgag | 0.5407919 |
| 6 | PASK_106_0 | PASK | gtatatgctcatctgagtga | 0.2050875 |
| 1 | PASK_0_0 | PASK | ggatgctgagaagcctcacc | 0.1610815 |
| 3 | PASK_0_6309 | PASK | gatgcttctgtgccctggac | 0.0893763 |
| 7 | PASK_108_25236 | PASK | gaaagccaagacatcttcac | -0.2255927 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000171219
HGNC SYMBOL (links to GeneCards) CDC42BPG
GENE DESCRIPTION
CDC42 binding protein kinase gamma (DMPK-like) [Source:HGNC Symbol;Acc:HGNC:29829]
GO TERM
cell leading edge
MIM GENE DESCRIPTION
CDC42-BINDING PROTEIN KINASE, GAMMA; CDC42BPG;;MYOTONIC DYSTROPHY KINASE-RELATED CDC42-BINDING KINASE, GAMMA; MRCKG;;MRCK-GAMMA
ENSEMBL PROTEIN ID
ENSP00000345133
PROTEIN FAMILY DESCRIPTION
SERINE/THREONINE KINASE MRCK EC_2.7.11.1 CDC42 BINDING KINASE DMPK MYOTONIC DYSTROPHY KINASE RELATED CDC42 BINDING KINASE MRCK MYOTONIC DYSTROPHY KINASE
Wilcox p-value: 0.8749233
DESeq2 p-value: 0.06333045
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 16 | CDC42BPG_102_15130 | CDC42BPG | ggaccgtctcccgcccgagc | 0.6054159 |
| 7 | CDC42BPG_100_15130 | CDC42BPG | ggacacctccaactttgatg | 0.4953713 |
| 5 | CDC42BPG_100_0 | CDC42BPG | ggggaggggtgcagtgggcg | 0.0525458 |
| 13 | CDC42BPG_101_18156 | CDC42BPG | ggtcaccgtggtgaggcaga | 0.0405820 |
| 6 | CDC42BPG_100_12104 | CDC42BPG | ggagctggagcagctacgga | 0.0139267 |
| 2 | CDC42BPG_0_15130 | CDC42BPG | gttgtctggcttgacatccc | -0.0573332 |
| 15 | CDC42BPG_102_0 | CDC42BPG | gagggagtctggagaacaaa | -0.2284839 |
| 4 | CDC42BPG_0_9078 | CDC42BPG | gtagaggctgtgttggcagt | -0.2611705 |
| 8 | CDC42BPG_100_18156 | CDC42BPG | gtggtgaggcagagggacac | -0.3513528 |
| 10 | CDC42BPG_101_0 | CDC42BPG | gaacaaagggtcctttctct | -0.4051230 |
| 14 | CDC42BPG_101_6052 | CDC42BPG | gaggagctgccaccatcccg | -0.4346633 |
| 11 | CDC42BPG_101_12104 | CDC42BPG | gggtaccacctcccctccag | -0.5207291 |
| 1 | CDC42BPG_0_0 | CDC42BPG | ggccctaacagagggcatca | -0.5829203 |
| 3 | CDC42BPG_0_6052 | CDC42BPG | ggcccatcatcttgagctgt | -0.6444921 |
| 12 | CDC42BPG_101_15130 | CDC42BPG | gctgggttatgtccacaggt | -0.6687819 |
| 9 | CDC42BPG_100_6052 | CDC42BPG | ggagctgccaccatcccgcg | -1.2168444 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000149554
HGNC SYMBOL (links to GeneCards) CHEK1
GENE DESCRIPTION
checkpoint kinase 1 [Source:HGNC Symbol;Acc:HGNC:1925]
GO TERM
replication fork
MIM GENE DESCRIPTION
CHECKPOINT, S. POMBE, HOMOLOG OF, 1; CHEK1;;CELL CYCLE CHECKPOINT KINASE; CHK1
ENSEMBL PROTEIN ID
ENSP00000388648
PROTEIN FAMILY DESCRIPTION
SERINE/THREONINE KINASE CHK1 EC_2.7.11.1 CHK1 CHECKPOINT HOMOLOG CHECKPOINT KINASE 1
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1231337
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 8 | CHEK1_116_0 | CHEK1 | gatgttgccgctcccgccca | 0.8004400 |
| 15 | CHEK1_132_43812 | CHEK1 | gaaatatgcctaggcatggt | 0.4073559 |
| 4 | CHEK1_101_0 | CHEK1 | gaccgcgctgcgcttccagg | 0.3253318 |
| 1 | CHEK1_0_14604 | CHEK1 | gagccacaatgccctgccat | 0.2268288 |
| 10 | CHEK1_11_0 | CHEK1 | ggagctggttcacagaaaaa | 0.1493467 |
| 3 | CHEK1_100_21906 | CHEK1 | gttgttgatatagtaaccta | 0.0000000 |
| 2 | CHEK1_0_29208 | CHEK1 | gtaagcaaaactttggggaa | -0.0097152 |
| 12 | CHEK1_120_0 | CHEK1 | gaatgtcggcggctccaaaa | -0.0418202 |
| 11 | CHEK1_11_7302 | CHEK1 | ggatatcaacatgacttttg | -0.0444676 |
| 14 | CHEK1_12_0 | CHEK1 | gagggcagaatttcaacctt | -0.0732607 |
| 5 | CHEK1_105_0 | CHEK1 | gcccaggcctccaagcctca | -0.3542135 |
| 9 | CHEK1_118_0 | CHEK1 | gcggctccaaaagggtgacg | -0.4289122 |
| 6 | CHEK1_10_0 | CHEK1 | gtaaagcattgttttggagc | -0.5804622 |
| 13 | CHEK1_121_0 | CHEK1 | gcttttcccgccaaaacttg | -0.7653539 |
| 7 | CHEK1_115_0 | CHEK1 | gcccagggctgctttgcagt | -1.4143340 |
| 16 | CHEK1_13_0 | CHEK1 | gcaagagctgttaattttcg | -1.6893490 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000182578
HGNC SYMBOL (links to GeneCards) CSF1R
GENE DESCRIPTION
colony stimulating factor 1 receptor [Source:HGNC Symbol;Acc:HGNC:2433]
GO TERM
CSF1-CSF1R complex
MIM GENE DESCRIPTION
COLONY-STIMULATING FACTOR 1 RECEPTOR; CSF1R;;MCSFR;;ONCOGENE FMS; FMS;;c-FMS;;CD115 ANTIGEN; CD115;;V-FMS MCDONOUGH FELINE SARCOMA VIRAL ONCOGENE HOMOLOG, FORMERLY
ENSEMBL PROTEIN ID
ENSP00000445282
PROTEIN FAMILY DESCRIPTION
MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT PRECURSOR SCFR EC_2.7.10.1 PROTO ONCOGENE C KIT TYROSINE KINASE KIT
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1115685
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 15 | CSF1R_117_25749 | CSF1R | ggcctcggtggggaagtggc | 0.7432286 |
| 7 | CSF1R_109_17166 | CSF1R | gtctgggcccattcagcaca | 0.6694507 |
| 1 | CSF1R_0_0 | CSF1R | gtgtggccagccacatgcca | 0.1437269 |
| 9 | CSF1R_10_0 | CSF1R | gataggacagaggatgccca | 0.0229662 |
| 5 | CSF1R_103_17166 | CSF1R | ggcctgtcctaaagagacct | -0.0440560 |
| 12 | CSF1R_114_25749 | CSF1R | gctcttaccatgccaagctg | -0.0897533 |
| 4 | CSF1R_101_17166 | CSF1R | gcttcaggcggggcagagag | -0.1942767 |
| 6 | CSF1R_106_17166 | CSF1R | gagggtgaaggtgtgcctgc | -0.3364257 |
| 10 | CSF1R_10_25749 | CSF1R | ggcagggtctagagtagagg | -0.3598989 |
| 11 | CSF1R_111_0 | CSF1R | gtgcagctcctgactattcc | -0.4741526 |
| 8 | CSF1R_109_8583 | CSF1R | gactcatgttggcatacagt | -0.5012091 |
| 2 | CSF1R_0_25749 | CSF1R | gggcactgcattgatagtcc | -0.5221593 |
| 3 | CSF1R_100_17166 | CSF1R | gccctgggatgactgagacc | -0.6523193 |
| 13 | CSF1R_115_25749 | CSF1R | gccaagctgtggccaccagc | -0.8383244 |
| 14 | CSF1R_116_8583 | CSF1R | gacatgcaggcgaccaccac | -0.8513914 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000142875
HGNC SYMBOL (links to GeneCards) PRKACB
GENE DESCRIPTION
protein kinase, cAMP-dependent, catalytic, beta [Source:HGNC Symbol;Acc:HGNC:9381]
GO TERM
transferase activity, transferring phosphorus-containing groups
MIM GENE DESCRIPTION
PROTEIN KINASE, cAMP-DEPENDENT, CATALYTIC, BETA; PRKACB
ENSEMBL PROTEIN ID
ENSP00000378314
PROTEIN FAMILY DESCRIPTION
CAMP DEPENDENT KINASE CATALYTIC SUBUNIT PKA C EC_2.7.11.11
Wilcox p-value: 0.9671744
DESeq2 p-value: 1.054877e-06
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 11 | PRKACB_122_114595 | PRKACB | gataattttatatcccacat | 0.4588957 |
| 1 | PRKACB_0_114595 | PRKACB | gctacaataaggcagtggat | 0.2836619 |
| 5 | PRKACB_117_91676 | PRKACB | gtgaaaacatttcaccccca | 0.0988086 |
| 12 | PRKACB_125_22919 | PRKACB | gccaaatcatcttatatgtc | 0.0802308 |
| 9 | PRKACB_120_114595 | PRKACB | gttcatatcaaaagttctgc | 0.0000000 |
| 13 | PRKACB_127_137514 | PRKACB | gtctgcaagggccaattctt | 0.0000000 |
| 4 | PRKACB_117_114595 | PRKACB | ggttggtctgcaaagaatgg | -0.0384741 |
| 10 | PRKACB_121_114595 | PRKACB | gtcattcttctaaggtgccc | -0.1305172 |
| 7 | PRKACB_11_0 | PRKACB | gacatgttagcacttaaagt | -0.3644069 |
| 8 | PRKACB_11_137514 | PRKACB | gggagacatcctcactttcc | -0.4000529 |
| 6 | PRKACB_118_22919 | PRKACB | gcactactagcattgcatga | -0.6499614 |
| 14 | PRKACB_134_137514 | PRKACB | gtacacactgctgctagtga | -0.7959443 |
| 3 | PRKACB_105_0 | PRKACB | gccggtgctaaggagttcgc | -0.9016024 |
| 15 | PRKACB_137_68757 | PRKACB | gtcaggagagtacttctacc | -0.9260958 |
| 2 | PRKACB_101_91676 | PRKACB | gttggatcattacagacagc | -0.9308058 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000185737
HGNC SYMBOL (links to GeneCards) NRG3
GENE DESCRIPTION
neuregulin 3 [Source:HGNC Symbol;Acc:HGNC:7999]
GO TERM
embryo development
MIM GENE DESCRIPTION
NEUREGULIN 3; NRG3
ENSEMBL PROTEIN ID
ENSP00000441201
PROTEIN FAMILY DESCRIPTION
PRO NEUREGULIN 3 MEMBRANE BOUND PRECURSOR PRO NRG3 [CONTAINS NEUREGULIN 3 NRG 3 ]
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.0723033
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 11 | NRG3_1458_953040 | NRG3 | gagggccttgtccaaaattc | 0.7452361 |
| 5 | NRG3_1334_953040 | NRG3 | gcctcatatcgatgcatcat | 0.5369936 |
| 15 | NRG3_1482_635360 | NRG3 | gctgttcaaactcccaaaga | 0.1508644 |
| 14 | NRG3_1478_0 | NRG3 | gctgccgatatgtaaatgaa | 0.0479055 |
| 7 | NRG3_1366_953040 | NRG3 | gtggcactttcagctgctct | 0.0444479 |
| 4 | NRG3_1193_476520 | NRG3 | ggccagttgtcttcaaaccc | 0.0000000 |
| 10 | NRG3_1445_635360 | NRG3 | gccataacagatgttcctct | 0.0000000 |
| 2 | NRG3_1160_794200 | NRG3 | gggctagctctctaaccata | -0.0736764 |
| 6 | NRG3_1364_317680 | NRG3 | gcgctcaaaccctttactgg | -0.4276937 |
| 12 | NRG3_1470_0 | NRG3 | gacctcagatggaaccagaa | -0.5988079 |
| 9 | NRG3_140_953040 | NRG3 | gaatcctaggtccctatacc | -0.6191415 |
| 13 | NRG3_1476_0 | NRG3 | gcagttctccagtccatgac | -0.6572912 |
| 3 | NRG3_1167_317680 | NRG3 | gaactcaacgtagaccatct | -0.6823694 |
| 8 | NRG3_1369_794200 | NRG3 | gtctgctacagtgtctcact | -0.7381306 |
| 1 | NRG3_1156_158840 | NRG3 | ggccagaatctctagcactt | -0.8424093 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000166484
HGNC SYMBOL (links to GeneCards) MAPK7
GENE DESCRIPTION
mitogen-activated protein kinase 7 [Source:HGNC Symbol;Acc:HGNC:6880]
GO TERM
negative regulation of NFAT protein import into nucleus
MIM GENE DESCRIPTION
MITOGEN-ACTIVATED PROTEIN KINASE 7; MAPK7;;PROTEIN KINASE, MITOGEN-ACTIVATED, 7; PRKM7;;EXTRACELLULAR SIGNAL-REGULATED KINASE 5; ERK5
ENSEMBL PROTEIN ID
ENSP00000311005
PROTEIN FAMILY DESCRIPTION
MITOGEN ACTIVATED KINASE 7 MAP KINASE 7 MAPK 7 EC_2.7.11.24 BIG MAP KINASE 1 BMK 1 EXTRACELLULAR SIGNAL REGULATED KINASE 5 ERK 5
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1051081
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 9 | MAPK7_10_4986 | MAPK7 | ggactgtggggagaggttcc | 1.3398243 |
| 6 | MAPK7_10_1662 | MAPK7 | gatggccacctgctggcctg | 0.8788394 |
| 11 | MAPK7_11_1662 | MAPK7 | gtcaccacatcgaaagcatt | 0.2509378 |
| 4 | MAPK7_0_4986 | MAPK7 | gtgttctcaggcacaccaaa | 0.1995151 |
| 14 | MAPK7_11_4155 | MAPK7 | ggccaaaggaaaatgggttc | 0.0717681 |
| 8 | MAPK7_10_4155 | MAPK7 | ggtctgggccaaaggaaaat | 0.0412438 |
| 2 | MAPK7_0_3324 | MAPK7 | gcgcattaaggaggccattg | -0.2006852 |
| 7 | MAPK7_10_3324 | MAPK7 | gggagacttggacttggaca | -0.3209398 |
| 12 | MAPK7_11_2493 | MAPK7 | ggtgactttggtatggctcg | -0.3341234 |
| 10 | MAPK7_10_831 | MAPK7 | ggctcggttctctgaaactc | -0.4125705 |
| 3 | MAPK7_0_4155 | MAPK7 | gttggaacgctggactcgaa | -0.5507305 |
| 5 | MAPK7_0_831 | MAPK7 | gcctacccctcccccgaccc | -0.6895103 |
| 15 | MAPK7_11_4986 | MAPK7 | gtgcaggagacatgcacctg | -0.9092088 |
| 13 | MAPK7_11_3324 | MAPK7 | ggctcctgagcctcggaagc | -0.9935284 |
| 1 | MAPK7_0_1662 | MAPK7 | gccccgcaggggagttgtga | -1.0384330 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000126453
HGNC SYMBOL (links to GeneCards) BCL2L12
GENE DESCRIPTION
BCL2-like 12 (proline rich) [Source:HGNC Symbol;Acc:HGNC:13787]
GO TERM
MIM GENE DESCRIPTION
BCL2-LIKE 12; BCL2L12
ENSEMBL PROTEIN ID
ENSP00000478415
PROTEIN FAMILY DESCRIPTION
BCL 2 12 BCL2 L 12 BCL 2 RELATED PROLINE RICH
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.01822949
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 7 | BCL2L12_36_3576 | BCL2L12 | gaccagcttgctgcgcaggg | 0.9538659 |
| 5 | BCL2L12_34_3576 | BCL2L12 | ggggtccgaggccagctgta | 0.8589222 |
| 13 | BCL2L12_8_4768 | BCL2L12 | ggcccgcctggccctagcca | 0.2415422 |
| 9 | BCL2L12_38_3576 | BCL2L12 | ggcggaccagcttgctgcgc | 0.1920837 |
| 1 | BCL2L12_15_7152 | BCL2L12 | gccacttttcccttccagga | 0.0261568 |
| 12 | BCL2L12_42_4768 | BCL2L12 | gctccacgctgagtccggcc | -0.1073999 |
| 10 | BCL2L12_38_7152 | BCL2L12 | gccctcctggaagggaaaag | -0.1755512 |
| 2 | BCL2L12_32_3576 | BCL2L12 | ggccagctgtagggtggaag | -0.4318455 |
| 11 | BCL2L12_39_7152 | BCL2L12 | gccaggatgccctcctggaa | -0.5109398 |
| 3 | BCL2L12_32_4768 | BCL2L12 | gctccatggctagggccagg | -0.7531135 |
| 4 | BCL2L12_33_3576 | BCL2L12 | gtccgaggccagctgtaggg | -0.7994554 |
| 6 | BCL2L12_35_3576 | BCL2L12 | gctgcgcagggcggggtccg | -0.9113653 |
| 8 | BCL2L12_37_3576 | BCL2L12 | gcggaccagcttgctgcgca | -1.9067631 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000137825
HGNC SYMBOL (links to GeneCards) ITPKA
GENE DESCRIPTION
inositol-trisphosphate 3-kinase A [Source:HGNC Symbol;Acc:HGNC:6178]
GO TERM
positive regulation of dendritic spine morphogenesis
MIM GENE DESCRIPTION
INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE A; ITPKA
ENSEMBL PROTEIN ID
ENSP00000260386
PROTEIN FAMILY DESCRIPTION
INOSITOL TRISPHOSPHATE 3 KINASE EC_2.7.1.127 INOSITOL 1 4 5 TRISPHOSPHATE 3 KINASE IP3 3 KINASE IP3K INSP 3 KINASE
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1123445
MAGeCK p-value: 0.701894
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 3 | ITPKA_0_7250 | ITPKA | gctgatcctgaagcgctgct | 0.7576987 |
| 9 | ITPKA_12_5800 | ITPKA | gtgtacttcagagaggacac | 0.5788964 |
| 14 | ITPKA_15_5800 | ITPKA | gggatgctctcaagattagc | 0.4267269 |
| 4 | ITPKA_0_8700 | ITPKA | gcgaggacggctatttgctg | 0.3086007 |
| 5 | ITPKA_10_1450 | ITPKA | ggccaatttagggcttcccc | 0.0961843 |
| 15 | ITPKA_16_2900 | ITPKA | gtgtcttcaaggcttccgaa | 0.0250445 |
| 13 | ITPKA_15_2900 | ITPKA | ggcatgagcaggtgtcttca | 0.0000000 |
| 12 | ITPKA_14_8700 | ITPKA | ggaggctctgccctctccag | -0.0364790 |
| 2 | ITPKA_0_2900 | ITPKA | gaggatgttcaagcttctcc | -0.0990264 |
| 7 | ITPKA_11_2900 | ITPKA | ggcttttcctaaccagccag | -0.2495652 |
| 6 | ITPKA_10_8700 | ITPKA | ggaccaggtgccagccacta | -0.5905395 |
| 11 | ITPKA_13_8700 | ITPKA | gggcaaagggcttcttcctc | -0.7691593 |
| 1 | ITPKA_0_0 | ITPKA | gcgaggacgtgggtcaggta | -0.8777683 |
| 10 | ITPKA_12_8700 | ITPKA | gccaggggttttgcccaccc | -0.9386408 |
| 8 | ITPKA_11_8700 | ITPKA | gaccaggtgccagccactaa | -0.9836681 |
| 16 | ITPKA_16_7250 | ITPKA | ggacatgtacaagaaaatgc | -1.0849872 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000101049
HGNC SYMBOL (links to GeneCards) SGK2
GENE DESCRIPTION
serum/glucocorticoid regulated kinase 2 [Source:HGNC Symbol;Acc:HGNC:13900]
GO TERM
positive regulation of transporter activity
MIM GENE DESCRIPTION
SERUM/GLUCOCORTICOID-REGULATED KINASE 2; SGK2
ENSEMBL PROTEIN ID
ENSP00000392795
PROTEIN FAMILY DESCRIPTION
SERINE/THREONINE KINASE EC_2.7.11.1 SERUM/GLUCOCORTICOID REGULATED KINASE
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.04938286
MAGeCK p-value: 0.79024
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 7 | SGK2_103_8362 | SGK2 | ggctccccatctgtataatg | 0.6581153 |
| 12 | SGK2_107_0 | SGK2 | gttttccactaacgtcatag | 0.3187377 |
| 1 | SGK2_0_25086 | SGK2 | gagtccaggactggcaggac | 0.1458818 |
| 10 | SGK2_106_25086 | SGK2 | ggtgaacaagacttgaggaa | 0.0372740 |
| 13 | SGK2_107_25086 | SGK2 | gggtgaacaagacttgagga | -0.0304471 |
| 2 | SGK2_100_4181 | SGK2 | ggaacaccatctcaccctag | -0.1618814 |
| 3 | SGK2_101_0 | SGK2 | gcctctcacctgaaaactcc | -0.2146417 |
| 4 | SGK2_101_4181 | SGK2 | gactggagacttctgttccc | -0.5254519 |
| 8 | SGK2_104_0 | SGK2 | gctaaaaccgctatagtcct | -0.5363070 |
| 5 | SGK2_101_8362 | SGK2 | ggctttcaggaaaaccagcc | -0.5808980 |
| 11 | SGK2_106_4181 | SGK2 | gggggctagctgatgtcacg | -0.6085201 |
| 9 | SGK2_105_4181 | SGK2 | ggggctagctgatgtcacgc | -0.9623739 |
| 6 | SGK2_102_0 | SGK2 | gaatcctcagcactgagcac | -1.2491888 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000127564
HGNC SYMBOL (links to GeneCards) PKMYT1
GENE DESCRIPTION
protein kinase, membrane associated tyrosine/threonine 1 [Source:HGNC Symbol;Acc:HGNC:29650]
GO TERM
MIM GENE DESCRIPTION
PROTEIN KINASE, MEMBRANE-ASSOCIATED TYROSINE/THREONINE, 1; PKMYT1;;CDC2-INHIBITORY KINASE, MEMBRANE-ASSOCIATED TYROSINE/THREONINE, 1;MYT1
ENSEMBL PROTEIN ID
ENSP00000461628
PROTEIN FAMILY DESCRIPTION
UNKNOWN
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.8398297
MAGeCK p-value: 0.79024
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 2 | PKMYT1_0_10722 | PKMYT1 | ggggtgacctccgcagcttc | 0.8814200 |
| 13 | PKMYT1_105_5361 | PKMYT1 | ggctggctcaccctgccagc | 0.7427912 |
| 14 | PKMYT1_105_7148 | PKMYT1 | gtgggtaccacctcccttcc | 0.1817254 |
| 11 | PKMYT1_104_5361 | PKMYT1 | gccagctggctacagcccct | 0.1005956 |
| 4 | PKMYT1_0_8935 | PKMYT1 | ggtgccactcagaggtggcg | -0.0288452 |
| 3 | PKMYT1_0_7148 | PKMYT1 | gctcaaagcctgccagcctg | -0.0485978 |
| 7 | PKMYT1_102_5361 | PKMYT1 | ggatgacgacagcctagggt | -0.0722303 |
| 12 | PKMYT1_104_7148 | PKMYT1 | ggaggacggccggctctatg | -0.2154798 |
| 6 | PKMYT1_101_7148 | PKMYT1 | ggcccgcaagttggccgagg | -0.3074704 |
| 15 | PKMYT1_106_5361 | PKMYT1 | ggcaggtaagctcccgacag | -0.3181115 |
| 1 | PKMYT1_0_0 | PKMYT1 | gcccggatgcacagttctga | -0.3338034 |
| 10 | PKMYT1_103_7148 | PKMYT1 | gcgttccatgtcaccattcc | -0.4395002 |
| 5 | PKMYT1_100_7148 | PKMYT1 | gcccgcaagttggccgaggt | -0.4400416 |
| 9 | PKMYT1_103_5361 | PKMYT1 | gggatgacgacagcctaggg | -0.7124507 |
| 8 | PKMYT1_102_7148 | PKMYT1 | gtcaccattccggggcccca | -0.8879269 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000164896
HGNC SYMBOL (links to GeneCards) FASTK
GENE DESCRIPTION
Fas-activated serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:24676]
GO TERM
protein phosphorylation
MIM GENE DESCRIPTION
FAS-ACTIVATED SERINE/THREONINE KINASE; FASTK;;FAST
ENSEMBL PROTEIN ID
ENSP00000444498
PROTEIN FAMILY DESCRIPTION
FAS ACTIVATED SERINE/THREONINE KINASE FAST KINASE EC_2.7.11.8
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1427661
MAGeCK p-value: 0.79024
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 13 | FASTK_10_3636 | FASTK | gccaatcccgaagcagctat | 1.0609902 |
| 5 | FASTK_0_3030 | FASTK | gcactggggcctcctccaac | 0.4466181 |
| 10 | FASTK_10_1818 | FASTK | ggccaggagcaccatcacgt | 0.3911856 |
| 4 | FASTK_0_2424 | FASTK | gagacatgtaaagtatcatg | 0.3431926 |
| 3 | FASTK_0_1818 | FASTK | ggtgtgtctgcttcaggaaa | 0.3339876 |
| 9 | FASTK_10_1212 | FASTK | gcatgctgctgacaggaggt | 0.2198671 |
| 15 | FASTK_11_0 | FASTK | gctggtagcccatcaggcct | -0.1872616 |
| 1 | FASTK_0_0 | FASTK | gggcctggagcttctgcctc | -0.2910421 |
| 7 | FASTK_0_606 | FASTK | gtccttgtgactgaggagaa | -0.4000973 |
| 6 | FASTK_0_3636 | FASTK | gacggtgctgggttccatgc | -0.4481787 |
| 2 | FASTK_0_1212 | FASTK | gccaggatcctctcaaggca | -0.5365657 |
| 14 | FASTK_10_606 | FASTK | gaggggtgcctgtggggagg | -0.5394610 |
| 11 | FASTK_10_2424 | FASTK | gagcaggagcaagcgttcct | -0.5862362 |
| 16 | FASTK_11_1212 | FASTK | ggaagcaggggtggcacccc | -0.6413484 |
| 8 | FASTK_10_0 | FASTK | gcaggagctggtagcccatc | -0.7574409 |
| 12 | FASTK_10_3030 | FASTK | gcgcgcccaccactactcgg | -1.4239192 |
In addition to the plots below, the following information has been retrieved via biomaRt:
ENSEMBL ID (links to Ensembl) ENSG00000106992
HGNC SYMBOL (links to GeneCards) AK1
GENE DESCRIPTION
adenylate kinase 1 [Source:HGNC Symbol;Acc:HGNC:361]
GO TERM
MIM GENE DESCRIPTION
ADENYLATE KINASE 1; AK1;;ADENYLATE KINASE, SOLUBLE
ENSEMBL PROTEIN ID
ENSP00000448741
PROTEIN FAMILY DESCRIPTION
UNKNOWN
Wilcox p-value: 0.9671744
DESeq2 p-value: 0.1097052
MAGeCK p-value: 0.79024
| designs | genes | sequence | log2Foldchange | |
|---|---|---|---|---|
| 10 | AK1_2_0 | AK1 | ggaacatatgctcagagcga | 1.0119537 |
| 9 | AK1_21_0 | AK1 | gcttaaagggagcccagctt | 0.6911687 |
| 4 | AK1_14_0 | AK1 | gaacggagggttgaggggct | 0.3342489 |
| 14 | AK1_3_0 | AK1 | gaacatatgctcagagcgat | 0.0280782 |
| 11 | AK1_37_0 | AK1 | gtcaaaaaatgaaagcgcgc | 0.0000000 |
| 2 | AK1_10_0 | AK1 | gggtccacaagaggctctct | -0.0714469 |
| 7 | AK1_1_0 | AK1 | ggatttcattcgggcaggcg | -0.0968484 |
| 13 | AK1_39_0 | AK1 | gcaggaagggttctccccag | -0.1320204 |
| 3 | AK1_12_0 | AK1 | gaggggtggctggcaaaggg | -0.3372427 |
| 15 | AK1_40_0 | AK1 | gggttctccccaggggattc | -0.3427298 |
| 16 | AK1_41_0 | AK1 | ggttctccccaggggattct | -0.3996150 |
| 5 | AK1_15_0 | AK1 | gttgaggggctggggacttg | -0.4933369 |
| 12 | AK1_38_0 | AK1 | gcgcaggaagggttctcccc | -0.5140515 |
| 6 | AK1_17_0 | AK1 | gcacatgaatcaactccaac | -0.6116374 |
| 8 | AK1_20_0 | AK1 | ggcttaaagggagcccagct | -0.6754054 |
| 1 | AK1_0_0 | AK1 | gtgcagtccaggccccggca | -0.6771400 |
On the following pages, a comparison between the hit analysis methods is generated.
List
Moreover, the 5 % top enriched hits sorted according to MAGeCK are stored in TRAILscreen-COMPARE-HITS.xls and are listed below:
| wilcox.log2fc | wilcox.pval | deseq.log2fc | deseq.pval | mageck.fdr | mageck.rank | |
|---|---|---|---|---|---|---|
| CASP8 | 2.8382733 | 0.0178241 | 2.8539899 | 0.0000000 | 0.001650 | 1 |
| BAX | 2.4706303 | 0.0178241 | 2.0761255 | 0.0000000 | 0.001650 | 2 |
| FADD | 2.8332735 | 0.0184341 | 2.7466780 | 0.0000000 | 0.001650 | 3 |
| PASK | 1.3650980 | 0.0178241 | 1.3056495 | 0.0000001 | 0.003713 | 4 |
| TYRO3 | 1.0116807 | 0.9671744 | 0.6568340 | 1.0000000 | 0.659241 | 5 |
| AMHR2 | 1.4654422 | 0.9671744 | 1.5964273 | 0.0000000 | 0.659241 | 6 |
| FN3K | 1.4685534 | 0.4030853 | 1.2257973 | 0.0000044 | 0.661245 | 7 |
| PRKY | 1.2424191 | 0.9671744 | 1.1629272 | 0.0000322 | 0.785149 | 8 |
| CDK5RAP3 | 0.8994121 | 0.4202992 | 0.6707720 | 0.4964897 | 0.785149 | 9 |
| ROR2 | 0.6903593 | 0.9671744 | 0.4127949 | 1.0000000 | 0.785149 | 10 |
| BMPR1A | 1.6970986 | 0.9671744 | 1.6606699 | 0.0000000 | 0.785149 | 11 |
| DGKI | 1.0784097 | 1.0000000 | 0.8176321 | 0.0921921 | 0.785149 | 12 |
| IP6K3 | 1.3336231 | 0.8019777 | 0.9775242 | 0.0004042 | 0.785149 | 13 |
| SGK1 | 1.0084174 | 0.9671744 | 1.0027240 | 0.0169285 | 0.785149 | 14 |
| CSNK1A1 | 0.9112430 | 0.9802939 | 0.2043810 | 1.0000000 | 0.785149 | 15 |
| RPS6KA5 | 1.0125970 | 0.9671744 | 2.0613922 | 0.0000000 | 0.792340 | 16 |
| FGFR2 | 0.9059273 | 0.9802939 | 0.6981811 | 0.2598086 | 0.792340 | 17 |
| FER | 0.9117190 | 0.9671744 | 0.8130390 | 0.0356230 | 0.792340 | 18 |
| GAK | 0.5387169 | 0.9671744 | 0.1504273 | 1.0000000 | 0.792340 | 19 |
| MYC | 0.9824296 | 0.9671744 | 1.0493447 | 0.0000603 | 0.819189 | 20 |
| NME7 | 1.0651572 | 0.9671744 | 0.7293105 | 1.0000000 | 0.819189 | 21 |
| MAP3K13 | 0.8027186 | 0.9802939 | 0.7890949 | 0.1618026 | 0.903465 | 22 |
| CDK17 | 1.4075806 | 0.9671744 | 1.9749507 | 0.0000000 | 0.903465 | 23 |
| UCK1 | 0.9366588 | 0.9671744 | 0.8130611 | 0.0389347 | 0.903465 | 24 |
| SPA17 | 0.9005421 | 0.4030853 | 0.6442567 | 0.7318362 | 0.903465 | 25 |
| STK32A | 0.7202280 | 0.9671744 | 0.5301267 | 1.0000000 | 0.903465 | 26 |
| MVK | 0.8969374 | 0.9671744 | 0.5232427 | 1.0000000 | 0.912769 | 27 |
| BIRC5 | 1.0329737 | 1.0000000 | 0.4600186 | 1.0000000 | 0.912769 | 28 |
| MAP2K7 | 1.4371620 | 1.0000000 | 1.1032489 | 0.0001706 | 0.912769 | 29 |
| TNFRSF8 | 0.9060177 | 0.9820183 | 0.8932955 | 1.0000000 | 0.919967 | 30 |
| RIPK2 | 1.0454989 | 0.9671744 | 0.9771641 | 0.0006398 | 0.987129 | 31 |
| MAP2K3 | 0.6951014 | 1.0000000 | 0.5789501 | 1.0000000 | 0.987129 | 32 |
| CDK9 | 1.0234281 | 0.9820183 | 0.6566444 | 1.0000000 | 0.987129 | 33 |
| DUSP10 | 0.9243816 | 0.9671744 | 0.8461876 | 0.6000355 | 0.987129 | 34 |
| LMTK3 | 1.4188888 | 1.0000000 | 1.0154113 | 0.0001587 | 0.987129 | 35 |
| TK2 | 0.8383299 | 0.9671744 | 0.4435478 | 1.0000000 | 0.987129 | 36 |
| NLK | 0.8116484 | 0.9671744 | 0.7749996 | 1.0000000 | 0.987129 | 37 |
| PRKD2 | 0.8994031 | 0.9671744 | 0.5585946 | 1.0000000 | 0.987129 | 38 |
| PRPS1 | 1.2220187 | 0.9802939 | 1.0154924 | 0.0010360 | 0.987129 | 39 |
| SGK223 | 0.7552550 | 1.0000000 | 0.5012950 | 1.0000000 | 0.987129 | 40 |
| SRPK2 | 0.7442764 | 0.9671744 | 0.8655405 | 0.0257051 | 0.987129 | 41 |
List
Moreover, the 5 % top depleted hits sorted according to __MAGeCK_ are stored in TRAILscreen-COMPARE-HITS.xls and are listed below:
| wilcox.log2fc | wilcox.pval | deseq.log2fc | deseq.pval | mageck.fdr | mageck.rank | |
|---|---|---|---|---|---|---|
| TNFRSF13C | NA | NA | -0.0773572 | 1.0000000 | 0.701894 | 1 |
| DYRK2 | NA | NA | -0.1075289 | 1.0000000 | 0.701894 | 2 |
| CDC42BPG | -0.1892980 | 0.8749233 | -0.9735155 | 0.0633304 | 0.701894 | 3 |
| CHEK1 | -0.0937255 | 0.9671744 | -0.8384986 | 0.1231337 | 0.701894 | 4 |
| RAPGEF3 | NA | NA | NA | NA | 0.701894 | 5 |
| TNFRSF11A | NA | NA | NA | NA | 0.701894 | 6 |
| CSF1R | -0.1386295 | 0.9671744 | -0.7419327 | 0.1115685 | 0.701894 | 7 |
| PTK6 | -0.0624989 | 0.9671744 | -0.4113096 | 1.0000000 | 0.701894 | 8 |
| BMF | NA | NA | -0.3582229 | 1.0000000 | 0.701894 | 9 |
| TESK2 | NA | NA | -0.4762269 | 1.0000000 | 0.701894 | 10 |
| NUAK2 | NA | NA | NA | NA | 0.701894 | 11 |
| AURKA | NA | NA | -0.1312312 | 1.0000000 | 0.701894 | 12 |
| PRKACB | -0.2086010 | 0.9671744 | -1.3268439 | 0.0000011 | 0.701894 | 13 |
| NRG3 | -0.1267339 | 0.9671744 | -0.7790845 | 0.0723033 | 0.701894 | 14 |
| TNFRSF13B | NA | NA | -0.1269107 | 1.0000000 | 0.701894 | 15 |
| AZU1 | -0.1144076 | 0.9671744 | -0.6156798 | 1.0000000 | 0.701894 | 16 |
| WIF1 | -0.0661615 | 0.9671744 | -0.8396864 | 0.0242731 | 0.701894 | 17 |
| MAPK7 | -0.0149634 | 0.9671744 | -0.7443061 | 0.1051081 | 0.701894 | 18 |
| HK3 | NA | NA | -0.8896877 | 0.0161867 | 0.701894 | 19 |
| BCL2L12 | -0.0770045 | 0.9671744 | -0.8493349 | 0.0182295 | 0.701894 | 20 |
| TP53BP1 | NA | NA | -0.0432170 | 1.0000000 | 0.701894 | 21 |
| ITPKA | -0.0990443 | 0.9671744 | -0.9804692 | 0.1123445 | 0.701894 | 22 |
| JAK3 | NA | NA | NA | NA | 0.701894 | 23 |
| CSNK1A1L | NA | NA | -0.4230571 | 1.0000000 | 0.736436 | 24 |
| PAK7 | NA | NA | -0.2202468 | 1.0000000 | 0.736436 | 25 |
| MAP3K6 | NA | NA | NA | NA | 0.790240 | 26 |
| CAMK1G | NA | NA | -0.4575927 | 1.0000000 | 0.790240 | 27 |
| PFKFB1 | NA | NA | -0.2941408 | 1.0000000 | 0.790240 | 28 |
| SGK2 | -0.1958993 | 0.9671744 | -0.7987094 | 0.0493829 | 0.790240 | 29 |
| PRKAA1 | NA | NA | -0.5851408 | 1.0000000 | 0.790240 | 30 |
| PKMYT1 | -0.0488289 | 0.9671744 | -0.6395897 | 0.8398297 | 0.790240 | 31 |
| TSSK3 | NA | NA | -0.4741866 | 1.0000000 | 0.790240 | 32 |
| NTRK3 | NA | NA | -0.1207013 | 1.0000000 | 0.790240 | 33 |
| FASTK | -0.0655226 | 0.9671744 | -0.8297426 | 0.1427661 | 0.790240 | 34 |
| AK1 | -0.0566054 | 0.9671744 | -0.7584758 | 0.1097052 | 0.790240 | 35 |
| CLK3 | NA | NA | -0.4754391 | 1.0000000 | 0.808760 | 36 |
| MAPKAPK5 | NA | NA | NA | NA | 0.808760 | 37 |
| PTPRG | NA | NA | -0.2841110 | 1.0000000 | 0.808760 | 38 |
| CDC42SE2 | NA | NA | -0.1443949 | 1.0000000 | 0.808760 | 39 |
| ACVRL1 | NA | NA | -0.4256669 | 1.0000000 | 0.808760 | 40 |
| PAPSS1 | NA | NA | -0.4826401 | 1.0000000 | 0.808760 | 41 |
A final table with all information for each gene is stored in
./data/TRAILscreen_FINAL.xls.
Hit candidates are annotated with additional information from biomaRt.
The following information is retrieved: Database: ensembl Dataset: hsapiens_gene_ensembl Filters: ensembl_gene_id description name_1006
The annotated list of all hit candidates is stored in
_ ./data _
** TRAILscreen_ANNOTATION.xls **
| Dataset | .fastq file name | Description |
|---|---|---|
| Control #1 | 2180_CRISPR_KO3_Drug_DMSO1_extracted-designs.txt | Control #1 |
| Control #2 | 2277_CRISPR_KO3_Drug_DMSO2_extracted-designs.txt | Control #2 |
| Treatment #1 | 2176_CRISPR_KO3_Drug_TRAIL1_extracted-designs.txt | TRAIL #1 |
| Treatment #2 | 2275_CRISPR_KO3_Drug_TRAIL2_extracted-designs.txt | TRAIL #2 |
The data is located in
./data
and the script files for data extraction and mapping are located in
./scripts.
All file-based output (e.g. tables) from MAGeCK is stored in:
/Users/janwinter/Documents/PhD/GitHub/caRpools.
| Parameter | Value |
|---|---|
| Reverse Complement Sequence | FALSE |
| Pattern of Data Extraction | ACC(.{20})GT{2,4}AGAGC |
| Maschine Identifier FASTq | M01100 |
| Create Bowtie2 Index? | FALSE |
| Reference .fasta File | pilot-screen-library |
| Bt2 Threads | 4 |
| Bt2 Sensitivity | very-sensitive-local |
| sgRNA Oligo Match | perfect |